X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FProbconsWS.java;h=5b933550936b9d720edca6ee4084d01130e097bc;hb=45154567757138fa61f345bee3429246a98f1969;hp=85e8a705c44e1b290ad530258e11363b3cb6b60f;hpb=2a269830633463e5016d5c92ed672d9e312c9776;p=jabaws.git

diff --git a/webservices/compbio/ws/server/ProbconsWS.java b/webservices/compbio/ws/server/ProbconsWS.java
index 85e8a70..5b93355 100644
--- a/webservices/compbio/ws/server/ProbconsWS.java
+++ b/webservices/compbio/ws/server/ProbconsWS.java
@@ -21,18 +21,18 @@ package compbio.ws.server;
 import java.io.File;
 import java.util.List;
 
-import javax.annotation.Resource;
 import javax.jws.WebService;
-import javax.xml.ws.WebServiceContext;
 
 import org.apache.log4j.Logger;
 
+import compbio.data.msa.JABAService;
 import compbio.data.msa.MsaWS;
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.FastaSequence;
 import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
 import compbio.engine.client.ConfiguredExecutable;
+import compbio.engine.client.SkeletalExecutable;
 import compbio.metadata.ChunkHolder;
 import compbio.metadata.JobStatus;
 import compbio.metadata.JobSubmissionException;
@@ -47,21 +47,15 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;
 import compbio.runner.msa.Probcons;
 
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ProbconsWS")
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ProbconsWS")
 public class ProbconsWS implements MsaWS<Probcons> {
 
-	// Ask for resource injection
-	@Resource
-	WebServiceContext wsContext;
-
-	private static Logger statLog = Logger.getLogger("ProbconsWS-stats");
-
 	private static Logger log = Logger.getLogger(ProbconsWS.class);
 
 	private static final RunnerConfig<Probcons> probconsOptions = Util
 			.getSupportedOptions(Probcons.class);
 
-	private static final LimitsManager<Probcons> limitMan = compbio.runner.Util
+	private static final LimitsManager<Probcons> limitMan = compbio.engine.client.Util
 			.getLimits(new Probcons().getType());
 
 	@Override
@@ -76,7 +70,9 @@ public class ProbconsWS implements MsaWS<Probcons> {
 	ConfiguredExecutable<Probcons> init(List<FastaSequence> dataSet)
 			throws JobSubmissionException {
 		Probcons probcons = new Probcons();
-		probcons.setInput("fasta.in").setOutput("alignment.out");
+		probcons.setInput(SkeletalExecutable.INPUT)
+				.setOutput(SkeletalExecutable.OUTPUT)
+				.setError(SkeletalExecutable.ERROR);
 		return Configurator.configureExecutable(probcons, dataSet);
 	}
 
@@ -123,6 +119,10 @@ public class ProbconsWS implements MsaWS<Probcons> {
 
 	@Override
 	public Limit<Probcons> getLimit(String presetName) {
+		if (limitMan == null) {
+			// Limit is not defined
+			return null;
+		}
 		return limitMan.getLimitByName(presetName);
 	}